The evolutionary history ofXiphophorusfish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

HYBRID SPECIATION AND INDEPENDENT EVOLUTION IN LINEAGES OF ALPINE BUTTERFLIES

(2012) Chris C. Nice et al.   EVOLUTION

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

(2012) JULIA C. JONES et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Introgression: An Integral but neglected component of speciation in birds

(2011) Frank E. Rheindt et al.   AUK

Mustached males in a tropical poeciliid fish: emerging female preference selects for a novel male trait

(2011) Ellen McCoy et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

(2011) Mark P. Simmons   CLADISTICS

Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids

(2011) Yingjia Shen et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

(2011) PAUL A. HOHENLOHE et al.   Molecular Ecology Resources

Evolutionary relationship between marble trout of the northern and the southern Adriatic basin

(2011) G. Pustovrh et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

(2011) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

(2011) P. A. Hohenlohe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Determination of Onset of Sexual Maturation and Mating Behavior by Melanocortin Receptor 4 Polymorphisms

(2010) Kathrin P. Lampert et al.   CURRENT BIOLOGY

Replicated hybrid zones of Xiphophorus swordtails along an elevational gradient

(2010) Z. W. CULUMBER et al.   MOLECULAR ECOLOGY

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

(2010) EVA-MARIA WILLING et al.   MOLECULAR ECOLOGY

Monophyletic origin of multiple clonal lineages in an asexual fish (Poecilia formosa)

(2010) MATTHIAS STÖCK et al.   MOLECULAR ECOLOGY

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: Evidence for introgressive hybridization and mitochondrial DNA capture

(2009) F. Barbanera et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

Evolution ofXmrk: an oncogene, but also a speciation gene?

(2008) Manfred Schartl   BIOESSAYS

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Surfing during population expansions promotes genetic revolutions and structuration

(2008) Laurent Excoffier et al.   TRENDS IN ECOLOGY & EVOLUTION